A conventional fuel cell system generally includes a fuel cell and a secondary cell. The conventional fuel cell system further has an idle stop function in which the fuel cell is stopped from generating electricity and power is supplied to a load only from the secondary cell under a prescribed condition. As shown in Japanese Patent Laid-Open Publication No. 2005-26054, when the fuel cell once again starts to generate electricity after the idle stop function is performed, it is determined whether there is any deterioration in the performance of the fuel cell (e.g., response delay in electricity generation or cell voltage drop). Although falling under the prescribed condition, if it is determined that there is deterioration in the performance then the conventional fuel cell system does not perform the idle stop function (i.e., stopping the fuel cell from generating electricity) and maintains the electricity generation of the fuel cell.